Author: "Fabien Ferrage" - Searchworks@Jio Institute Digital Library Search Results

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89 results on '"Fabien Ferrage"'

1. Two-field transverse relaxation-optimized spectroscopy for the study of large biomolecules – An in silico investigation

Author: Nicolas Bolik-Coulon, Philippe Pelupessy, Guillaume Bouvignies, and Fabien Ferrage
Subjects: Two-field NMR, Protein NMR, TROSY, Fluorine NMR, Aromatic side chains, Medical physics. Medical radiology. Nuclear medicine, R895-920, Physics, QC1-999
Abstract: Biomolecular NMR spectroscopy has greatly benefited from the development of TROSY-type pulse sequences, in pair with specific labeling. The selection of spin operators with favorable relaxation properties has led to an increase in the resolution and sensitivity of spectra of large biomolecules. However, nuclei with a large chemical shift anisotropy (CSA) contribution to relaxation can still suffer from large linewidths at conventional magnetic fields (higher than 9 T). Here, we introduce the concept of two-field TROSY (2F-TROSY) where the chemical shifts of nuclei with large CSA is labeled at low fields (ca. 2 T) dramatically reducing the contribution of CSA to relaxation. Signal detection is performed at high field (> 9 T) on a nucleus with efficient TROSY interference to yield high resolution and sensitivity. We use comprehensive numerical simulations to demonstrate the power of this approach on aromatic 13C-19F spin pairs for which a TROSY pulse sequence has recently been published. We predict that the 2F-TROSY experiment shall yield good quality spectra for large proteins (global tumbling correlation times as high as 100 ns) with one order of magnitude higher sensitivity than the single-field experiment.
Published: 2020
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2. Identification of Hydrophobic Interfaces in Protein-Ligand Complexes by Selective Saturation Transfer NMR Spectroscopy

Author: Fabien Ferrage, Kaushik Dutta, and David Cowburn
Subjects: NMR, cross-saturation, SH3 ligand, interface identification, Organic chemistry, QD241-441
Abstract: The proper characterization of protein-ligand interfaces is essential for structural biology, with implications ranging from the fundamental understanding of biological processes to pharmacology. Nuclear magnetic resonance is a powerful technique for such studies. We propose a novel approach to the direct determination of the likely pose of a peptide ligand onto a protein partner, by using frequency-selective cross-saturation with a low stringency isotopic labeling methods. Our method illustrates a complex of the Src homology 3 domain of C-terminal Src kinase with a peptide from the proline-enriched tyrosine phosphatase.
Published: 2015
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3. Two‐Dimensional Methods and Zero‐ to Ultralow‐Field ( <scp>ZULF</scp> ) <scp>NMR</scp>

Author: K. Ivanov, John Blanchard, Dmitry Budker, Fabien Ferrage, Alexey Kiryutin, Tobias Sjolander, Alexandra Yurkovskaya, and Ivan Zhukov
Published: 2023

4. Introduction to 'Geoffrey Bodenhausen Festschrift'

Author: Daniel Abergel and Fabien Ferrage
Subjects: Condensed Matter Physics, Atomic and Molecular Physics, and Optics, Analytical Chemistry
Published: 2023

5. Comprehensive analysis of relaxation decays from high-resolution relaxometry

Author: Nicolas Bolik-Coulon, Milan Zachrdla, Guillaume Bouvignies, Philippe Pelupessy, and Fabien Ferrage
Abstract: Relaxometry consists in measuring relaxation rates over orders of magnitude of magnetic fields to probe motions of complex systems. High-resolution relaxometry (HRR) experiments can be performed on conventional high-field NMR magnets equipped with a sample shuttle. During the experiment, the sample shuttle transfers the sample between the high-field magnetic center and a chosen position in the stray field for relaxation during a variable delay, thus using the stray field as a variable field. As the relaxation delay occurs outside of the probe, HRR experiments cannot rely on the control of cross-relaxation pathways, which is standard in high-field relaxation pulse sequences. Thus, decay rates are not pure relaxation rates, which may impair a reliable description of the dynamics. Previously, we took into account cross-relaxation effects in the analysis of high- resolution relaxometry data by applying a correction factor to relaxometry decay rates in order to estimate relaxation rates. These correction factors were obtained from the iterative simulation of the relaxation decay while the sample lies outside of the probe and a preceding analysis of relaxation rates which relies on the approximation of a priori multi-exponential decays by mono-exponential functions. However, an analysis protocol matching directly experimental and simulated relaxometry decays should be more self consistent. Here, we introduce Matching INtensities for the Optimization of Timescales and Amplitudes of motions Under Relaxometry (MINOTAUR), a framework for the analysis of high-resolution relaxometry that takes as input the intensity decays at all fields. This approach uses the full relaxation matrix to calculate intensity decays, allowing complex relaxation pathways to be taken into account. Therefore, it eliminates the need for a correction of decay rates and for fitting multi-exponential decays with mono-exponential functions. The MINOTAUR software is designed as a flexible framework where relaxation matrices and spectral density functions corresponding to various models of motions can be defined on a case-by-case basis. The agreement with our previous analyses of protein side-chain dynamics from carbon-13 relaxation is excellent, while providing a more robust analysis tool. We expect MINOTAUR to become the tool of choice for the analysis of high-resolution relaxometry.
Published: 2023

6. Convergent vews on disordered protein dynamics from NMR and computational approaches

Author: Nicola, Salvi, Vojtěch, Zapletal, Zuzana, Jaseňáková, Milan, Zachrdla, Petr, Padrta, Subhash, Narasimhan, Thorsten, Marquardsen, Jean-Max, Tyburn, Lukáš, Žídek, Martin, Blackledge, Fabien, Ferrage, Pavel, Kadeřávek, Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Masaryk University [Brno] (MUNI), Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Laboratoire des biomolécules (LBM UMR 7203), Chimie Moléculaire de Paris Centre (FR 2769), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Bruker BioSpin MRI GmbH [Ettlingen, Germany], ANR-18-CE29-0003,NANO-DISPRO,Une méthode intégrative pour déterminer les mouvements nanométriques des protéines désordonnées(2018), Ferrage, Fabien, and APPEL À PROJETS GÉNÉRIQUE 2018 - Une méthode intégrative pour déterminer les mouvements nanométriques des protéines désordonnées - - NANO-DISPRO2018 - ANR-18-CE29-0003 - AAPG2018 - VALID
Subjects: Intrinsically Disordered Proteins, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, [CHIM.THEO] Chemical Sciences/Theoretical and/or physical chemistry, Magnetic Resonance Spectroscopy, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Protein Conformation, [SDV.BBM.BS] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Biophysics, [SDV.BBM.BP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, DNA-Directed RNA Polymerases, Molecular Dynamics Simulation, Amides
Abstract: International audience; Intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs) is a class of biologically important proteins exhibiting specific biophysical characteristics. They lack a hydrophobic core, and their conformational behavior is strongly influenced by electrostatic interactions. IDPs and IDRs are highly dynamic, and a characterization of the motions of IDPs and IDRs is essential for their physically correct description. NMR together with molecular dynamics simulations are the methods best suited to such a task because they provide information about dynamics of proteins with atomistic resolution. Here, we present a study of motions of a disordered C-terminal domain of the delta subunit of RNA polymerase from Bacillus subtilis. Positively and negatively charged residues in the studied domain form transient electrostatic contacts critical for the biological function. Our study is focused on investigation of ps-ns dynamics of backbone of the delta subunit based on analysis of amide 15N NMR relaxation data and molecular dynamics simulations. In order to extend an informational content of NMR data to lower frequencies, which are more sensitive to slower motions, we combined standard (high-field) NMR relaxation experiments with high-resolution relaxometry. Altogether, we collected data reporting the relaxation at 12 different magnetic fields, resulting in an unprecedented data set. Our results document that the analysis of such data provides a consistent description of dynamics and confirms the validity of so far used protocols of the analysis of dynamics of IDPs also for a partially folded protein. In addition, the potential to access detailed description of motions at the timescale of tens of ns with the help of relaxometry data is discussed. Interestingly, in our case, it appears to be mostly relevant for a region involved in the formation of temporary contacts within the disordered region, which was previously proven to be biologically important.
Published: 2022

7. How does it really move? Recent progress in the investigation of protein nanosecond dynamics by NMR and simulation

Author: Olof Stenström, Candide Champion, Marc Lehner, Guillaume Bouvignies, Sereina Riniker, Fabien Ferrage, Laboratoire des biomolécules (LBM UMR 7203), Chimie Moléculaire de Paris Centre (FR 2769), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Chemistry and Applied Biosciences [ETH Zürich] (D-CHAB), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), and Ferrage, Fabien
Subjects: Magnetic Resonance Spectroscopy, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Molecular dynamics simulations, [SDV.BBM.BS] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], [SDV.BBM.BP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Protein dynamics, Molecular Dynamics Simulation, NMR spectroscopy, NMR relaxation, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, [CHIM.THEO] Chemical Sciences/Theoretical and/or physical chemistry, Motion, Structural Biology, Molecular Biology, Nuclear Magnetic Resonance, Biomolecular
Abstract: Nuclear magnetic resonance (NMR) spin relaxation experi-ments currently probe molecular motions on timescales from picoseconds to nanoseconds. The detailed interpretation of these motions in atomic detail benefits from complementarity with the results from molecular dynamics (MD) simulations. In this mini-review, we describe the recent developments in experimental techniques to study the backbone dynamics from 15N relaxation and side-chain dynamics from 13C relaxation, discuss the different analysis approaches from model-free to dynamics detectors, and highlight the many ways that NMR relaxation experiments and MD simulations can be used together to improve the interpretation and gain insights into protein dynamics. ISSN:0959-440X ISSN:1879-033X
Published: 2022

8. How wide is the window opened by high-resolution relaxometry on the internal dynamics of proteins in solution?

Author: Nicolas Bolik-Coulon, Matthias Ernst, Fabien Ferrage, Albert A. Smith, Beat H. Meier, Universität Leipzig [Leipzig], Laboratoire des biomolécules (LBM UMR 7203), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Chimie Moléculaire de Paris Centre (FR 2769), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)
Subjects: Relaxometry, 010402 general chemistry, 01 natural sciences, Biochemistry, Article, [CHIM]Chemical Sciences, Isoleucine, Nuclear Magnetic Resonance, Biomolecular, Spectroscopy, Detector analysis, Ubiquitin, 010405 organic chemistry, Chemistry, Protein dynamics, Resolution (electron density), Relaxation (NMR), Dynamics (mechanics), Detector, Proteins, Rotational diffusion, Nanosecond, Dynamics, 0104 chemical sciences, Solutions, Chemical physics, Solution-state NMR
Abstract: The dynamics of molecules in solution is usually quantified by the determination of timescale-specific amplitudes of motions. High-resolution nuclear magnetic resonance (NMR) relaxometry experiments—where the sample is transferred to low fields for longitudinal (T1) relaxation, and back to high field for detection with residue-specific resolution—seeks to increase the ability to distinguish the contributions from motion on timescales slower than a few nanoseconds. However, tumbling of a molecule in solution masks some of these motions. Therefore, we investigate to what extent relaxometry improves timescale resolution, using the “detector” analysis of dynamics. Here, we demonstrate improvements in the characterization of internal dynamics of methyl-bearing side chains by carbon-13 relaxometry in the small protein ubiquitin. We show that relaxometry data leads to better information about nanosecond motions as compared to high-field relaxation data only. Our calculations show that gains from relaxometry are greater with increasing correlation time of rotational diffusion., Journal of Biomolecular NMR, 75 (2-3), ISSN:0925-2738, ISSN:1573-5001
Published: 2021

9. The soft breeze of the cation atmosphere around DNA

Author: Fabien Ferrage and Damien Laage
Subjects: Atmosphere, Cations, Biophysics, DNA
Published: 2022

10. Explicit models of motions to understand protein side-chain dynamics

Author: Nicolas Bolik-Coulon, Olivier Languin-Cattoën, Diego Carnevale, Milan Zachrdla, Damien Laage, Fabio Sterpone, Guillaume Stirnemann, Fabien Ferrage, Laboratoire des biomolécules (LBM UMR 7203), Chimie Moléculaire de Paris Centre (FR 2769), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de biochimie théorique [Paris] (LBT (UPR_9080)), Institut de biologie physico-chimique (IBPC (FR_550)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Processus d'Activation Sélective par Transfert d'Energie Uni-électronique ou Radiatif (UMR 8640) (PASTEUR), Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Ferrage, Fabien
Subjects: Diffusion, Chemical Physics (physics.chem-ph), [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Motion, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], [SDV.BBM.BS] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Entropy, Physics - Chemical Physics, General Physics and Astronomy, FOS: Physical sciences, [SDV.BBM.BP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Molecular Dynamics Simulation
Abstract: International audience; Nuclear magnetic relaxation is widely used to probe protein dynamics. For decades, most analyses of relaxation in proteins have relied successfully on the model-free approach, forgoing mechanistic descriptions of motions. Model-free types of correlation functions cannot describe a large carbon-13 relaxation dataset in protein sidechains. Here, we use molecular dynamics simulations to design explicit models of motion and solve Fokker-Planck diffusion equations. These models of motion provide better agreement with relaxation data, mechanistic insight and a direct link to configuration entropy.
Published: 2022

11. Explicit models of motions to analyze NMR relaxation data in proteins

Author: Nicolas Bolik-Coulon and Fabien Ferrage
Subjects: Chemical Physics (physics.chem-ph), Motion, Magnetic Resonance Spectroscopy, Physics - Chemical Physics, Proteins, General Physics and Astronomy, FOS: Physical sciences, Molecular Dynamics Simulation, Physical and Theoretical Chemistry, Magnetic Resonance Imaging, Nuclear Magnetic Resonance, Biomolecular
Abstract: Nuclear Magnetic Resonance (NMR) is a tool of choice to characterize molecular motions. In biological macromolecules, pico- to nanosecond motions, in particular, can be probed by nuclear spin relaxation rates, which depend on the time fluctuations of the orientations of spin interaction frames. For the past 40 years, relaxation rates have been successfully analyzed using the Model-Free (MF) approach, which makes no assumption on the nature of motions and reports on the effective amplitude and timescale of the motions. However, obtaining a mechanistic picture of motions from this type of analysis is difficult at best, unless complemented with molecular dynamics (MD) simulations. In spite of their limited accuracy, such simulations can be used to obtain the information necessary to build explicit models of motions designed to analyze NMR relaxation data. Here, we present how to build such models, suited in particular to describe motions of methyl-bearing protein side chains and compare them with the MF approach. We show on synthetic data that explicit models of motions are more robust in the presence of rotamer jumps which dominate the relaxation in methyl groups of protein side chains. We expect this work to motivate the use of explicit models of motion to analyze MD and NMR data.
Published: 2022
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12. Protein Dynamics from Accurate Low-Field Site-Specific Longitudinal and Transverse Nuclear Spin Relaxation

Author: Jean-Nicolas Dumez, Jean-Max Tyburn, Samuel F. Cousin, Fabien Ferrage, Pavel Kadeřávek, Nicolas Bolik-Coulon, Thorsten Marquardsen, Laboratoire des biomolécules (LBM UMR 7203), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Chimie Moléculaire de Paris Centre (FR 2769), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Bruker Biospin GmbH, bruker, Bruker BioSpin [Wissembourg], Chimie Et Interdisciplinarité : Synthèse, Analyse, Modélisation (CEISAM), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Chimie Moléculaire de Paris Centre (FR 2769), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Nantes (UN)-Université de Nantes (UN)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Dumez, Jean-Nicolas
Subjects: 0301 basic medicine, 030103 biophysics, Relaxometry, Field (physics), [SDV.BBM.BP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, 010402 general chemistry, 01 natural sciences, Molecular physics, Motion, 03 medical and health sciences, low-field NMR spectroscopy, General Materials Science, Physical and Theoretical Chemistry, Nuclear Magnetic Resonance, Biomolecular, Larmor precession, Physics, Carbon Isotopes, Ubiquitin, Protein dynamics, Demagnetizing field, Relaxation (NMR), Proteins, Nanosecond, 0104 chemical sciences, Magnetic field, high-field NMR spectroscopy, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, [CHIM.THEO] Chemical Sciences/Theoretical and/or physical chemistry, nuclear magnetic resonance, Kinetics, Magnetic Fields, NMR relaxation, protein dynamics, Protons
Abstract: International audience; Nuclear magnetic relaxation provides invaluable quantitative site-specific information on the dynamics of complex systems. Determining dynamics on nanosecond timescales requires relaxation measurements at low magnetic fields, incompatible with high-resolution NMR. Here, we use a two-field NMR spectrometer to measure carbon-13 transverse and longitudinal relaxation rates at a field as low as 0.33 T (proton Larmor frequency 14 MHz) in specifically labeled sidechains of the protein ubiquitin. The use of radiofrequency pulses enhances the accuracy of measurements as compared to high-resolution relaxometry approaches, where the sample is moved in the stray field of the superconducting magnet. Importantly, we demonstrate that accurate measurements at a single low magnetic field provide enough information to characterize complex motions on low nanosecond timescales, which opens a new window for the determination of site-specific nanosecond motions in complex systems such as proteins.
Published: 2019

13. Sequential assignment of NMR spectra of peptides at natural isotopic abundance with zero- and ultra-low-field total correlation spectroscopy (ZULF-TOCSY)

Author: Ivan V. Zhukov, Geoffrey Bodenhausen, Alexey S. Kiryutin, Konstantin L. Ivanov, Alexandra V. Yurkovskaya, Fabien Ferrage, Laboratoire des biomolécules (LBM UMR 7203), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: Magnetic Resonance Spectroscopy, Field (physics), Chemistry, Enkephalin, Methionine, Spectrum Analysis, Relaxation (NMR), General Physics and Astronomy, Natural abundance, 02 engineering and technology, 021001 nanoscience & nanotechnology, 01 natural sciences, Spectral line, NMR spectra database, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Heteronuclear molecule, Chemical physics, 0103 physical sciences, [CHIM]Chemical Sciences, Physical and Theoretical Chemistry, 010306 general physics, 0210 nano-technology, Spectroscopy, Macromolecule
Abstract: A novel method dubbed ZULF-TOCSY results from the combination of Zero and Ultra-Low Field (ZULF) with high-field, high-resolution NMR, leading to a generalization of the concept of total correlation spectroscopy (TOCSY). ZULF-TOCSY is a new building block for NMR methods, which has the unique property that the polarization is evenly distributed among all NMR-active nuclei such as 1H, 13C, 15N, 31P, etc., provided that they belong to the same coupling network, and provided that their relaxation is not too fast at low fields, as may occur in macromolecules. Here, we show that ZULF-TOCSY correlations can be observed for peptides at natural isotopic abundance, such as the protected hexapeptide Boc-Met-enkephalin. The analysis of ZULF-TOCSY spectra readily allows one to make sequential assignments, thus offering an alternative to established heteronuclear 2D experiments like HMBC. For Boc-Met-enkephalin, we show that ZULF-TOCSY allows one to observe all expected cross-peaks between carbonyl carbons and α-CH protons, while the popular HMBC method provides insufficient information.
Published: 2021

14. Comment on mr-2021-4

Author: Fabien Ferrage
Published: 2021

15. Detection of Metabolite-Protein Interactions in Complex Biological Samples by High-Resolution Relaxometry: Towards Interactomics by NMR

Author: Veronica Ghini, Pavel Kaderavek, Fabien Ferrage, Jean-Max Tyburn, Guillaume Bouvignies, Thorsten Marquardsen, Morgan Kazmierczak, Ziqing Wang, Claudio Luchinat, Philippe Pelupessy, Giacomo Parigi, Simone Pisano, and Milan Zachrdla
Subjects: In situ, Relaxometry, chemistry.chemical_compound, Blood serum, Metabolomics, chemistry, Metabolite, Biophysics, Quantitative analysis (chemistry), Small molecule, Protein–protein interaction, 3. Good health
Abstract: In this manuscript, we introduce an NMR method to investigate the interaction of metabolites and other small molecules with proteins in biological fluids. Our approach, based on high-resolution relaxometry identifies the interaction of small molecules with proteins in blood serum and is used for the quantitative analysis of binding competition in situ.
Published: 2021

16. Detection of Metabolite–Protein Interactions in Complex Biological Samples by High-Resolution Relaxometry: Toward Interactomics by NMR

Author: Jean-Max Tyburn, Simone Pisano, Ziqing Wang, Veronica Ghini, Philippe Pelupessy, Morgan Kazmierczak, Giacomo Parigi, Thorsten Marquardsen, Fabien Ferrage, Guillaume Bouvignies, Claudio Luchinat, Pavel Kadeřávek, Milan Zachrdla, Laboratoire des biomolécules (LBM UMR 7203), Chimie Moléculaire de Paris Centre (FR 2769), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Università degli Studi di Siena = University of Siena (UNISI)-Università degli Studi di Firenze = University of Florence (UniFI)-University of Bologna/Università di Bologna-Partenaires INRAE, Structure et Dynamique des Biomolécules (LBM-E3), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Chimie Moléculaire de Paris Centre (FR 2769), Ecole Polytechnique Fédérale de Lausanne (EPFL), Bruker BioSpin MRI GmbH [Ettlingen, Germany], Università degli Studi di Firenze = University of Florence (UniFI), Gestionnaire, HAL Sorbonne Université 5, Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Chimie Moléculaire de Paris Centre (FR 2769), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Università degli Studi di Siena = University of Siena (UNISI)-Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI)-University of Bologna-Partenaires INRAE, Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, and Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI)
Subjects: Relaxometry, Human blood, Chemistry, Metabolite, High resolution, General Chemistry, Computational biology, 010402 general chemistry, 01 natural sciences, Biochemistry, Small molecule, Catalysis, NMR, 0104 chemical sciences, Protein–protein interaction, chemistry.chemical_compound, Colloid and Surface Chemistry, Metabolomics, [CHIM] Chemical Sciences, [CHIM]Chemical Sciences, Interactomics, Macromolecule
Abstract: International audience; Metabolomics, the systematic investigation of metabolites in biological fluids, cells or tissues, reveals essential information about metabolism and diseases. Metabolites have functional roles in myriads of biological processes, as substrates and products of enzymatic reactions, but also as cofactors and regulators of large numbers of biochemical mechanisms. These functions involve interactions of metabolites with macromolecules. Yet, methods to systematically investigate these interactions are hitherto still scarce. In particular, there is a need for techniques suited to identify and characterize weak metabolite-macromolecule interactions directly in complex media such as biological fluids. Here, we introduce a method to investigate weak interactions between metabolites and macromolecules in biological fluids. Our approach is based on high-resolution NMR relaxometry and does not require any invasive procedure or separation step. We show that we can detect interactions between small and large molecules in human blood serum and quantify the size of the complex. Our work opens the way for investigations of metabolite-(or other small molecules) protein interactions in biological fluids for interactomics or pharmaceutical applications.
Published: 2021
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17. A very interesting investigation on the effect of cross-relaxation on paramagnetic relaxation enhancements

Author: Fabien Ferrage
Subjects: Paramagnetism, Materials science, Condensed matter physics, Relaxation (physics), Cross relaxation
Published: 2020

18. Two-field transverse relaxation-optimized spectroscopy for the study of large biomolecules – An in silico investigation

Author: Fabien Ferrage, Nicolas Bolik-Coulon, Philippe Pelupessy, Guillaume Bouvignies, Laboratoire des biomolécules (LBM UMR 7203), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Chimie Moléculaire de Paris Centre (FR 2769), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), and Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: lcsh:Medical physics. Medical radiology. Nuclear medicine, Materials science, lcsh:R895-920, Fluorine-19 NMR, 010402 general chemistry, 01 natural sciences, Molecular physics, 03 medical and health sciences, Transverse relaxation-optimized spectroscopy, Anisotropy, Spin (physics), Aromatic side chains, 030304 developmental biology, Spin-½, 0303 health sciences, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], 010405 organic chemistry, Chemical shift, Relaxation (NMR), Pulse sequence, Nuclear magnetic resonance spectroscopy, Fluorine NMR, lcsh:QC1-999, 0104 chemical sciences, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Yield (chemistry), Two-field NMR, Protein NMR, TROSY, Order of magnitude, lcsh:Physics
Abstract: Biomolecular NMR spectroscopy has greatly benefited from the development of TROSY-type pulse sequences, in pair with specific labeling. The selection of spin operators with favorable relaxation properties has led to an increase in the resolution and sensitivity of spectra of large biomolecules. However, nuclei with a large chemical shift anisotropy (CSA) contribution to relaxation can still suffer from large linewidths at conventional magnetic fields (higher than 9 T). Here, we introduce the concept of two-field TROSY (2F-TROSY) where the chemical shifts of nuclei with large CSA is labeled at low fields (ca. 2 T) dramatically reducing the contribution of CSA to relaxation. Signal detection is performed at high field (> 9 T) on a nucleus with efficient TROSY interference to yield high-resolution and sensitivity. We use comprehensive numerical simulations to demonstrate the power of this approach on aromatic 13C-19F spin pairs for which a TROSY pulse sequence has recently been published. We predict that the 2F- TROSY experiment shall yield good quality spectra for large proteins (global tumbling correlation times as high as 100 ns) with one order of magnitude higher sensitivity than the single-field experiment.
Published: 2020

19. Surprising absence of strong homonuclear coupling at low magnetic field explored by two-field NMR spectroscopy

Author: Ivan V. Zhukov, Alexey S. Kiryutin, Ziqing Wang, Milan Zachrdla, Alexandra V. Yurkovskaya, Konstantin L. Ivanov, Fabien Ferrage, Laboratoire des biomolécules (LBM UMR 7203), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry
Abstract: Strong coupling of nuclear spins, which is achieved when their scalar coupling 2πJ is greater than or comparable to the difference δω in their Larmor precession frequencies in an external magnetic field, gives rise to efficient coherent longitudinal polarization transfer. The strong-coupling regime can be achieved when the external magnetic field is sufficiently low, as δω is reduced proportional to the field strength. In the present work, however, we demonstrate that in heteronuclear spin systems these simple arguments may not hold, since heteronuclear spin-spin interactions alter the δω value. The experimental method that we use is two-field NMR (Nuclear Magnetic Resonance), exploiting sample shuttling between a high field, at which NMR spectra are acquired, and low field, where strong couplings are expected, at which NMR pulses can be applied to affect the spin dynamics. By using this technique, we generate zero-quantum spin coherences by means of non-adiabatic passage through a level anti-crossing and study their evolution at low field. Such zero-quantum coherences mediate the polarization transfer under strong coupling conditions. Experiments performed with an 13C labelled amino acid clearly show that the coherent polarization transfer at low field is pronounced in the 13C-spin subsystem under proton decoupling. However, in the absence of proton decoupling, polarization transfer by coherent processes is dramatically reduced, demonstrating that heteronuclear spin-spin interactions suppress the strong coupling regime even when the external field is low. A theoretical model is presented, which can model the reported experimental results.
Published: 2020

20. Total Correlation Spectroscopy Across All NMR-Active Nuclei by Mixing at Zero Field

Author: Alexandra V. Yurkovskaya, Gerd Buntkowsky, Fabien Ferrage, Alexey S. Kiryutin, Konstantin L. Ivanov, Ivan V. Zhukov, Novosibirsk State University (NSU), International Tomography Center [Novosibirsk, Russia] ( SB RAS), Laboratoire des biomolécules (LBM UMR 7203), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Chimie Moléculaire de Paris Centre (FR 2769), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Technische Universität Darmstadt (TU Darmstadt), Ferrage, Fabien, Chimie Moléculaire de Paris Centre (FR 2769), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Technische Universität Darmstadt - Technical University of Darmstadt (TU Darmstadt)
Subjects: chemistry.chemical_classification, Physics, 010304 chemical physics, Spins, Biomolecule, Isotropy, 010402 general chemistry, Polarization (waves), 01 natural sciences, Spectral line, 0104 chemical sciences, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, [CHIM.THEO] Chemical Sciences/Theoretical and/or physical chemistry, Chemical bond, chemistry, Heteronuclear molecule, Chemical physics, 0103 physical sciences, General Materials Science, Physical and Theoretical Chemistry, Spectroscopy
Abstract: Multidimensional Nuclear Magnetic Resonance (NMR) is based on the combination of well-established building blocks for polarization transfer. These blocks are used to design correlation experiments through one or a few chemical bonds or through space. Here, we introduce a building block that enables polarization transfer across all NMR-active nuclei in a coupled network of spins: isotropic mixing at Zero and Ultra-Low Field (ZULF). Exploiting mixing under ZULF-NMR conditions, heteronuclear TOtal Correlation SpectroscopY (TOCSY) experiments were developed to highlight coupled spin networks. We demonstrate 1H-13C and 1H-15N correlations in ZULF-TOCSY spectra of labelled amino acids, which allow one to obtain cross-peaks among all hetero-nuclei belonging to the same coupled network, even when the direct interaction between them is negligible. We also demonstrate the interest of ZULF-TOCSY to analyze complex mixtures on the supernatant of ISOGRO, a growth medium of isotope-labelled biomolecules. ZULF-TOCSY enables the quick identification of individual compounds in the mixture by their coupled spin networks. The ZULF-TOCSY method will lead to the development of a new toolbox of experiments to analyze complex mixtures by NMR.
Published: 2020

21. Sensitivity-enhanced three-dimensional and carbon-detected two-dimensional NMR of proteins using hyperpolarized water

Author: Geoffrey Bodenhausen, Isabella C. Felli, Roberta Pierattelli, Borja Mateos, Dennis Kurzbach, Fabien Ferrage, Robert Konrat, Pavel Kadeřávek, Gregory L. Olsen, Lucio Frydman, Or Szekely, Laboratoire des biomolécules (LBM UMR 7203), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Chimie Moléculaire de Paris Centre (FR 2769), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), and Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Amide proton, 010402 general chemistry, Intrinsically disordered proteins, 01 natural sciences, Biochemistry, Article, Direct 13C detection, Humans, Hyperpolarization (physics), Non-uniform sampling, Spectroscopy, Nuclear Magnetic Resonance, Biomolecular, ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, 3D NMR, Spectrometer, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Ubiquitin, 010405 organic chemistry, Water, Polarization (waves), 0104 chemical sciences, Amino acid, Intrinsically Disordered Proteins, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Hyperpolarization, chemistry, BEST-HNCO, Chemical physics, Osteopontin, Dissolution-dynamic nuclear polarization (D-DNP), Order of magnitude
Abstract: Signal enhancements of up to two orders of magnitude in protein NMR can be achieved by employing HDO as a vector to introduce hyperpolarization into folded or intrinsically disordered proteins. In this approach, hyperpolarized HDO produced by dissolution-dynamic nuclear polarization (D-DNP) is mixed with a protein solution waiting in a high-field NMR spectrometer, whereupon amide proton exchange and nuclear Overhauser effects (NOE) transfer hyperpolarization to the protein and enable acquisition of a signal-enhanced high-resolution spectrum. To date, the use of this strategy has been limited to 1D and 1H-15N 2D correlation experiments. Here we introduce 2D 13C-detected D-DNP, to reduce exchange-induced broadening and other relaxation penalties that can adversely affect proton-detected D-DNP experiments. We also introduce hyperpolarized 3D spectroscopy, opening the possibility of D-DNP studies of larger proteins and IDPs, where assignment and residue-specific investigation may be impeded by spectral crowding. The signal enhancements obtained depend in particular on the rates of chemical and magnetic exchange of the observed residues, thus resulting in non-uniform ‘hyperpolarization-selective’ signal enhancements. The resulting spectral sparsity, however, makes it possible to resolve and monitor individual amino acids in IDPs of over 200 residues at acquisition times of just over a minute. We apply the proposed experiments to two model systems: the compactly folded protein ubiquitin, and the intrinsically disordered protein (IDP) osteopontin (OPN). Electronic supplementary material The online version of this article (10.1007/s10858-020-00301-5) contains supplementary material, which is available to authorized users.
Published: 2020

22. Boosting the resolution of low-field 15 N relaxation experiments on intrinsically disordered proteins with triple-resonance NMR

Author: Jean-Max Tyburn, Vojtěch Zapletal, Milan Zachrdla, Nicolas Bolik-Coulon, Pavel Kadeřávek, Petr Padrta, Zuzana Jaseňáková, Thorsten Marquardsen, Fabien Ferrage, Lukáš Žídek, Gestionnaire, Hal Sorbonne Université, Masaryk University [Brno] (MUNI), Laboratoire des biomolécules (LBM UMR 7203), Chimie Moléculaire de Paris Centre (FR 2769), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Chimie Moléculaire de Paris Centre (FR 2769), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), and Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: 0301 basic medicine, Relaxometry, [SDV.BBM.BS] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Nonuniform sampling, Relaxation, 010402 general chemistry, Intrinsically disordered proteins, 01 natural sciences, Biochemistry, Spectral line, Nuclear magnetic resonance, 03 medical and health sciences, Non-uniform sampling, Spectroscopy, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Chemistry, Chemical shift, Nuclear magnetic resonance spectroscopy, Nanosecond, 0104 chemical sciences, Magnetic field, Dynamics, 030104 developmental biology, High-resolution relaxometry
Abstract: Improving our understanding of nanosecond motions in disordered proteins requires the enhanced sampling of the spectral density function obtained from relaxation at low magnetic fields. High-resolution relaxometry and two-field NMR measurements of relaxation have, so far, only been based on the recording of one- or two-dimensional spectra, which provide insufficient resolution for challenging disordered proteins. Here, we introduce a 3D-HNCO-based two-field NMR experiment for measurements of protein backbone [Formula: see text] amide longitudinal relaxation rates. The experiment provides accurate longitudinal relaxation rates at low field (0.33 T in our case) preserving the resolution and sensitivity typical for high-field NMR spectroscopy. Radiofrequency pulses applied on six different radiofrequency channels are used to manipulate the spin system at both fields. The experiment was demonstrated on the C-terminal domain of [Formula: see text] subunit of RNA polymerase from Bacillus subtilis, a protein with highly repetitive amino-acid sequence and very low dispersion of backbone chemical shifts.
Published: 2020

23. Time-Resolved Protein Side-Chain Motions Unraveled by High-Resolution Relaxometry and Molecular Dynamics Simulations

Author: Lei Bruschweiler-Li, Yina Gu, Rafael Brüschweiler, Jean-Max Tyburn, Thorsten Marquardsen, Nicolas Bolik-Coulon, Cyril Charlier, Pavel Kadeřávek, Samuel F. Cousin, Ludovic Carlier, Fabien Ferrage, Structure et Dynamique des Biomolécules (LBM-E3), Laboratoire des biomolécules (LBM UMR 7203), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Chimie Moléculaire de Paris Centre (FR 2769), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC), Université Pierre et Marie Curie - Paris 6 (UPMC), Bruker Biospin GmbH, bruker, Bruker BioSpin [Wissembourg], Department of Chemistry and Biochemistry, and National High Magnetic Field Laboratory, Florida State University [Tallahassee] (FSU), Cousin, Samuel, Chimie Moléculaire de Paris Centre (FR 2769), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Chimie Moléculaire de Paris Centre (FR 2769), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Département de Chimie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Relaxometry, 010405 organic chemistry, Chemistry, General Chemistry, Conformational entropy, 01 natural sciences, Biochemistry, Catalysis, 0104 chemical sciences, Protein–protein interaction, 03 medical and health sciences, Molecular dynamics, 030104 developmental biology, Colloid and Surface Chemistry, Solid-state nuclear magnetic resonance, Chemical physics, [CHIM] Chemical Sciences, Side chain, [CHIM]Chemical Sciences, Molecule, Conformational isomerism, ComputingMilieux_MISCELLANEOUS
Abstract: Motions of proteins are essential for the performance of their functions. Aliphatic protein side chains and their motions play critical roles in protein interactions: for recognition and binding of partner molecules at the surface or serving as an entropy reservoir within the hydrophobic core. Here, we present a new NMR method based on high-resolution relaxometry and high-field relaxation to determine quantitatively both motional amplitudes and time scales of methyl-bearing side chains in the picosecond-to-nanosecond range. We detect a wide variety of motions in isoleucine side chains in the protein ubiquitin. We unambiguously identify slow motions in the low nanosecond range, which, in conjunction with molecular dynamics computer simulations, could be assigned to transitions between rotamers. Our approach provides unmatched detailed insight into the motions of aliphatic side chains in proteins and provides a better understanding of the nature and functional role of protein side-chain motions.
Published: 2018

24. Structure and Dynamics of an Intrinsically Disordered Protein Region That Partially Folds upon Binding by Chemical-Exchange NMR

Author: Aneel K. Aggarwal, Nicolas Bolik-Coulon, Fabien Ferrage, Ludovic Carlier, Philippe Pelupessy, Guillaume Bouvignies, Cyril Charlier, Sandrine Sagan, Rodrigue Marquant, Mikhail Kozlov, Astrid Walrant, Pablo De Ioannes, Patricia Cortes, Structure et Dynamique des Biomolécules (LBM-E3), Laboratoire des biomolécules (LBM UMR 7203), Université Pierre et Marie Curie - Paris 6 (UPMC)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Analyse, Interactions Moléculaires et Cellulaires (LBM-E2), Chimie Moléculaire de Paris Centre (FR 2769), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Chimie Moléculaire de Paris Centre (FR 2769), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Peptides, glycoconjugués et métaux en biologie (LBM-E1), Icahn School of Medicine at Mount Sinai [New York] (MSSM), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC), and HAL-UPMC, Gestionnaire
Subjects: 0301 basic medicine, Protein Folding, Protein Conformation, [SDV.BBM.BS] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Plasma protein binding, Crystallography, X-Ray, 010402 general chemistry, Intrinsically disordered proteins, 01 natural sciences, Biochemistry, Catalysis, DNA Ligase ATP, 03 medical and health sciences, Colloid and Surface Chemistry, Protein structure, Bound state, Nuclear Magnetic Resonance, Biomolecular, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Chemistry, Chemical shift, Relaxation (NMR), General Chemistry, 0104 chemical sciences, Intrinsically Disordered Proteins, Molecular Docking Simulation, Folding (chemistry), Crystallography, 030104 developmental biology, Protein folding, Protein Binding
Abstract: International audience; Many intrinsically disordered proteins (IDPs) and protein regions (IDRs) engage in transient, yet specific, interactions with a variety of protein partners. Often, if not always, interactions with a protein partner lead to partial folding of the IDR. Characterizing the conformational space of such complexes is challenging: in solution-‐state NMR, signals of the IDR in the interacting region become broad, weak and often invisible; while X-‐ray crystallography only provides information on fully ordered regions. There is thus a need for a simple method to characterize both fully and partially ordered regions in the bound state of IDPs. Here, we introduce an approach based on monitoring chemical ex-‐ change by NMR to investigate the state of an IDR that folds upon binding through the observation of the free state of the protein. Structural constraints for the bound state are obtained from chemical shifts and site-‐specific dynamics of the bound state are characterized by relaxation rates. The conformation of the interacting part of the IDR was determined and subsequently docked onto the structure of the folded partner. We apply the method to investigate the interaction between the disordered C-‐terminal region of Artemis and the DNA binding domain of Ligase IV. We show that we can accurately reproduce the structure of the core of the complex determined by X-‐ray crystallography and identify a broader interface. The method is widely applicable to the biophysical investigation of complexes of disordered proteins and folded proteins.
Published: 2017

25. Full Correlations across Broad NMR Spectra by Two‐Field Total Correlation Spectroscopy

Author: Geoffrey Bodenhausen, Léonard Strouk, Fabien Ferrage, Samuel F. Cousin, Werner Maas, Jean-Max Tyburn, Pierre-Alain Bovier, Pavel Kadeřávek, Cyril Charlier, Thorsten Marquardsen, Frank Engelke, Structure et Dynamique des Biomolécules (LBM-E3), Laboratoire des biomolécules (LBM UMR 7203), Université Pierre et Marie Curie - Paris 6 (UPMC)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Bruker Biospin GmbH, bruker, Bruker BioSpin [Wissembourg], Bruker Biospin AG, Bruker BioSpin GmbH, D-76287 Rheinstetten, Germany, affiliation inconnue, Bruker BioSpin [Billerica, MA], Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: Field (physics), 010405 organic chemistry, Chemistry, Chemical shift, Analytical chemistry, Nuclear magnetic resonance spectroscopy, Fluorine-19 NMR, 010402 general chemistry, 01 natural sciences, Atomic and Molecular Physics, and Optics, Spectral line, 0104 chemical sciences, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, NMR spectra database, Nuclear magnetic resonance, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Molecule, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], Physical and Theoretical Chemistry, Spectroscopy
Abstract: International audience; Total correlation spectroscopy (TOCSY) is a key experiment to assign nuclear magnetic resonance (NMR) spectra of complex molecules. Carbon-13 TOCSY experiments are essential to assign signals of protein side chains. However, the performance of carbon-13 TOCSY deteriorates at high magnetic fields since the necessarily limited radiofrequency irradiation fails to cover the broad range of carbon-13 frequencies. Here, we introduce a new concept to overcome the limitations of TOCSY by using two-field NMR spectroscopy. In two-field TOCSY experiments, chemical shifts are labelled at high field but isotropic mixing is performed at a much lower magnetic field, where the frequency range of the spectrum is drastically reduced. We obtain complete correlations between all carbon-13 nuclei belonging to amino acids across the entire spectrum: aromatic, aliphatic and carboxylic. Two-field TOCSY should be a robust and general approach for the assignment of uniformly carbon-13 labelled molecules in high-field and ultra-high field NMR spectrometers beyond 1000 MHz.
Published: 2017

26. Boosting the resolution of low-field [Formula: see text] relaxation experiments on intrinsically disordered proteins with triple-resonance NMR

Author: Zuzana, Jaseňáková, Vojtěch, Zapletal, Petr, Padrta, Milan, Zachrdla, Nicolas, Bolik-Coulon, Thorsten, Marquardsen, Jean-Max, Tyburn, Lukáš, Žídek, Fabien, Ferrage, and Pavel, Kadeřávek
Subjects: Intrinsically Disordered Proteins, Bacterial Proteins, DNA-Directed RNA Polymerases, Nuclear Magnetic Resonance, Biomolecular, Recombinant Proteins, Bacillus subtilis
Abstract: Improving our understanding of nanosecond motions in disordered proteins requires the enhanced sampling of the spectral density function obtained from relaxation at low magnetic fields. High-resolution relaxometry and two-field NMR measurements of relaxation have, so far, only been based on the recording of one- or two-dimensional spectra, which provide insufficient resolution for challenging disordered proteins. Here, we introduce a 3D-HNCO-based two-field NMR experiment for measurements of protein backbone [Formula: see text] amide longitudinal relaxation rates. The experiment provides accurate longitudinal relaxation rates at low field (0.33 T in our case) preserving the resolution and sensitivity typical for high-field NMR spectroscopy. Radiofrequency pulses applied on six different radiofrequency channels are used to manipulate the spin system at both fields. The experiment was demonstrated on the C-terminal domain of [Formula: see text] subunit of RNA polymerase from Bacillus subtilis, a protein with highly repetitive amino-acid sequence and very low dispersion of backbone chemical shifts.
Published: 2019

27. Protein Dynamics from Accurate Low-Field Site-Specific Longitudinal and Transverse Relaxation

Author: Nicolas Bolik-Coulon, Jean-Max Tyburn, Thorsten Marquardsen, Jean-Nicolas Dumez, Samuel F. Cousin, Pavel Kaderavek, and Fabien Ferrage
Subjects: Larmor precession, Physics, Relaxometry, Field (physics), Demagnetizing field, Relaxation (NMR), Superconducting magnet, Nanosecond, Molecular physics, Magnetic field
Abstract: Nuclear magnetic relaxation provides invaluable quantitative site-specific information on the dynamics of complex systems. Determining dynamics on nanosecond timescales requires relaxation measurements at low magnetic fields, incompatible with high-resolution NMR. Here, we use a two-field NMR spectrometer to measure carbon-13 transverse and longitudinal relaxation rates at a field as low as 0.33 T (proton Larmor frequency 14 MHz) in specifically labeled sidechains of the protein ubiquitin. The use of radiofrequency pulses enhances the accuracy of measurements as compared to high-resolution relaxometry approaches, where the sample is moved in the stray field of the superconducting magnet. Importantly, we demonstrate that accurate measurements at a single low magnetic field provide enough information to characterize complex motions on low nanosecond timescales, which opens a new window for the determination of site- specific nanosecond motions in complex systems such as proteins.
Published: 2019

28. Reducing bias in the analysis of solution-state NMR data with dynamics detectors

Author: Fabien Ferrage, Matthias Ernst, Beat H. Meier, Albert A. Smith, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Physical Chemistry [ETH Zürich], Department of Chemistry and Applied Biosciences [ETH Zürich] (D-CHAB), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)- Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), and Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: General Physics and Astronomy, FOS: Physical sciences, 010402 general chemistry, 01 natural sciences, Physics - Chemical Physics, 0103 physical sciences, Range (statistics), Sensitivity (control systems), Physical and Theoretical Chemistry, Nuclear Magnetic Resonance, Biomolecular, ComputingMilieux_MISCELLANEOUS, Physics, Chemical Physics (physics.chem-ph), 010304 chemical physics, Dynamics (mechanics), Relaxation (NMR), Detector, Proteins, 0104 chemical sciences, Computational physics, Exponential function, Magnetic field, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Correlation function (statistical mechanics), Thermodynamics
Abstract: The Journal of Chemical Physics, 151 (3), ISSN:0021-9606, ISSN:1089-7690
Published: 2019

29. Understanding the methyl-TROSY effect over a wide range of magnetic fields

Author: Nicolas Bolik-Coulon, Samuel F. Cousin, Jean-Nicolas Dumez, Fabien Ferrage, Pavel Kadeřávek, Laboratoire des biomolécules (LBM UMR 7203), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Chimie Moléculaire de Paris Centre (FR 2769), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Chimie Et Interdisciplinarité : Synthèse, Analyse, Modélisation (CEISAM), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), and Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)
Subjects: General Physics and Astronomy, FOS: Physical sciences, 010402 general chemistry, Interference (wave propagation), Rotation, 01 natural sciences, Molecular physics, Quantitative Biology::Cell Behavior, Physics - Chemical Physics, 0103 physical sciences, Physical and Theoretical Chemistry, Spectroscopy, ComputingMilieux_MISCELLANEOUS, Physics, Chemical Physics (physics.chem-ph), Range (particle radiation), 010304 chemical physics, Spectrometer, Quantitative Biology::Molecular Networks, Relaxation (NMR), equipment and supplies, 0104 chemical sciences, Magnetic field, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Transverse plane, human activities
Abstract: The use of relaxation interference in the methyl Transverse Relaxation-Optimized SpectroscopY (TROSY) experiment has opened new avenues for the study of large proteins and protein assemblies in nuclear magnetic resonance. So far, the theoretical description of the methyl-TROSY experiment has been limited to the slow-tumbling approximation, which is correct for large proteins on high-field spectrometers. In a recent paper, favorable relaxation interference was observed in the methyl groups of a small protein at a magnetic field as low as 0.33 T, well outside the slow-tumbling regime. Here, we present a model to describe relaxation interference in methyl groups over a broad range of magnetic fields, not limited to the slow-tumbling regime. We predict that the type of multiple-quantum transition that shows favorable relaxation properties change with the magnetic field. Under the condition of fast methyl-group rotation, methyl-TROSY experiments can be recorded over the entire range of magnetic fields from a fraction of 1 T up to 100 T.
Published: 2019

30. Contributors

Author: Martin Blackledge, Nicolas Bolik-Coulon, Guillaume Bouvignies, Ludovic Carlier, Charles W. Christoffer, Hoi Sung Chung, A. Keith Dunker, Santiago Esteban-Martin, Fabien Ferrage, Gustavo Fuertes, Alex S. Holehouse, Malene Ringkjøbing Jensen, Daisuke Kihara, Lukasz Kurgan, Laura Nevola, Christopher J. Oldfield, Nicola Salvi, Robert Schneider, Vladimir N. Uversky, and Wenwei Zheng
Published: 2019

31. Experimental characterization of the dynamics of IDPs and IDRs by NMR

Author: Nicolas Bolik-Coulon, Fabien Ferrage, Guillaume Bouvignies, Ludovic Carlier, Laboratoire des biomolécules (LBM UMR 7203), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Chimie Moléculaire de Paris Centre (FR 2769), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Ferrage, Fabien, Chimie Moléculaire de Paris Centre (FR 2769), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Physics, Millisecond, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], 010405 organic chemistry, [SDV.BBM.BS] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Dynamics (mechanics), Relaxation (NMR), [SDV.BBM.BP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, 010402 general chemistry, 01 natural sciences, 0104 chemical sciences, Characterization (materials science), [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, [CHIM.THEO] Chemical Sciences/Theoretical and/or physical chemistry, Chemical physics
Abstract: International audience; Nuclear Magnetic Resonance is a unique approach to obtain at the same time information on dynamics over a broad range of timescales and high-resolution information in disordered proteins. In this chapter, we will review the different methods available to characterize motions in disordered proteins. We first focus on dynamics in the picosecond-nanosecond range, which is characterized by nuclear spin relaxation measurements. We will focus then on slower processes, mostly in the millisecond range, studied by chemical-exchange NMR, discussing in particular the dynamics of the binding of disordered proteins to their targets and their dynamics in these complexes.
Published: 2019

32. Analysis of NMR Spin-Relaxation Data Using an Inverse Gaussian Distribution Function

Author: Fabien Ferrage, Arthur G. Palmer, Andrew Hsu, and Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: Data Analysis, 0301 basic medicine, Magnetic Resonance Spectroscopy, Saccharomyces cerevisiae Proteins, 030303 biophysics, Normal Distribution, Biophysics, Probability density function, 010402 general chemistry, 01 natural sciences, Normal distribution, Inverse Gaussian distribution, 03 medical and health sciences, symbols.namesake, Protein Domains, Statistical physics, ComputingMilieux_MISCELLANEOUS, Probability, Physics, 0303 health sciences, 030102 biochemistry & molecular biology, Correction, Proteins, Spectral density, Function (mathematics), 0104 chemical sciences, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Correlation function (statistical mechanics), Basic-Leucine Zipper Transcription Factors, Distribution function, symbols, Probability distribution
Abstract: Spin relaxation in solution-state NMR spectroscopy is a powerful approach to explore the conformational dynamics of biological macromolecules. Probability distribution functions for overall or internal correlation times have been used previously to model spectral density functions central to spin-relaxation theory. Applications to biological macromolecules rely on transverse relaxation rate constants, and when studying nanosecond timescale motions, sampling at ultralow frequencies is often necessary. Consequently, appropriate distribution functions necessitate spectral density functions that are accurate and convergent as frequencies approach zero. In this work, the inverse Gaussian probability distribution function is derived from general properties of spectral density functions at low and high frequencies for macromolecules in solution, using the principle of maximal entropy. This normalized distribution function is first used to calculate the correlation function, followed by the spectral density function. The resulting model-free spectral density functions are finite at a frequency of zero and can be used to describe distributions of either overall or internal correlation times using the model-free ansatz. To validate the approach, (15)N spin-relaxation data for the bZip transcription factor domain of the Saccharomyces cerevisiae protein GCN4, in the absence of cognate DNA, were analyzed using the inverse Gaussian probability distribution for intramolecular correlation times. The results extend previous models for the conformational dynamics of the intrinsically disordered, DNA-binding region of the bZip transcription factor domain.
Published: 2018

33. Recovering Invisible Signals by Two-Field NMR Spectroscopy

Author: Pierre-Alain Bovier, Werner Maas, Baptiste Haddou, Philippe Pelupessy, Thorsten Marquardsen, Cyril Charlier, Samuel F. Cousin, Jean-Max Tyburn, Frank Engelke, Fabien Ferrage, Geoffrey Bodenhausen, Pavel Kadeřávek, Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Structure et Dynamique des Biomolécules (LBM-E3), Laboratoire des biomolécules (LBM UMR 7203), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC), Université Pierre et Marie Curie - Paris 6 (UPMC), Processus d'Activation Sélective par Transfert d'Energie Uni-électronique ou Radiatif (UMR 8640) (PASTEUR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratory of Chemical Physics [Bethesda] (LCP), National Institutes of Health, Bruker Biospin GmbH, bruker, Bruker BioSpin [Wissembourg], Bruker Biospin AG, Bruker BioSpin GmbH, D-76287 Rheinstetten, Germany, affiliation inconnue, Bruker BioSpin [Billerica, MA], École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Département de Chimie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Carbon-13 NMR satellite, Chemistry, 010405 organic chemistry, General Chemistry, Fluorine-19 NMR, Nuclear magnetic resonance spectroscopy, Nuclear magnetic resonance crystallography, General Medicine, Carbon-13 NMR, 010402 general chemistry, Molecular physics, 01 natural sciences, Catalysis, 0104 chemical sciences, Nuclear magnetic resonance, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Transverse relaxation-optimized spectroscopy, Two-dimensional nuclear magnetic resonance spectroscopy, Earth's field NMR
Abstract: Nuclear magnetic resonance (NMR) studies have benefited tremendously from the steady increase in the strength of magnetic fields. Spectacular improvements in both sensitivity and resolution have enabled the investigation of molecular systems of rising complexity. At very high fields, this progress may be jeopardized by line broadening, which is due to chemical exchange or relaxation by chemical shift anisotropy. In this work, we introduce a two-field NMR spectrometer designed for both excitation and observation of nuclear spins in two distinct magnetic fields in a single experiment. NMR spectra of several small molecules as well as a protein were obtained, with two dimensions acquired at vastly different magnetic fields. Resonances of exchanging groups that are broadened beyond recognition at high field can be sharpened to narrow peaks in the low-field dimension. Two-field NMR spectroscopy enables the measurement of chemical shifts at optimal fields and the study of molecular systems that suffer from internal dynamics, and opens new avenues for NMR spectroscopy at very high magnetic fields.
Published: 2016

34. Protein dynamics from nuclear magnetic relaxation

Author: Fabien Ferrage, Cyril Charlier, Samuel F. Cousin, Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Université Pierre et Marie Curie - Paris 6 (UPMC), Structure et Dynamique des Biomolécules (LBM-E3), Laboratoire des biomolécules (LBM UMR 7203), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC), European Research Council (ERC) under the European Community, ERC [279519 (2F4BIODYN)], École normale supérieure - Paris (ENS-PSL), Université Pierre et Marie Curie - Paris 6 (UPMC)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Département de Chimie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Nuclear magnetic relaxation, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Protein Conformation, Chemistry, Movement, Protein dynamics, Proteins, General Chemistry, 010402 general chemistry, 01 natural sciences, Measure (mathematics), 0104 chemical sciences, 03 medical and health sciences, 030104 developmental biology, Nuclear magnetic resonance, Atomic resolution, Chemical physics, Picosecond, Molecular motion, Humans, Nuclear Magnetic Resonance, Biomolecular
Abstract: International audience; Nuclear magnetic resonance is a ubiquitous spectroscopic tool to explore molecules with atomic resolution. Nuclear magnetic relaxation is intimately connected to molecular motions. Many methods and models have been developed to measure and interpret the characteristic rates of nuclear magnetic relaxation in proteins. These approaches shed light on a rich and diverse range of motions covering timescales from picoseconds to seconds. Here, we introduce some of the basic concepts upon which these approaches are built and provide a series of illustrations.
Published: 2016

35. Theoretical and computational framework for the analysis of the relaxation properties of arbitrary spin systems. Application to high-resolution relaxometry

Author: Samuel F. Cousin, Pavel Kadeřávek, Philippe Pelupessy, Nicolas Bolik-Coulon, Jean-Nicolas Dumez, Fabien Ferrage, Laboratoire des biomolécules (LBM UMR 7203), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Chimie Moléculaire de Paris Centre (FR 2769), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Structure et Dynamique des Biomolécules (LBM-E3), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, Chimie Et Interdisciplinarité : Synthèse, Analyse, Modélisation (CEISAM), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), and Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)
Subjects: Nuclear and High Energy Physics, Relaxometry, Biophysics, FOS: Physical sciences, High resolution, Longitudinal Relaxation Rate, 010402 general chemistry, 01 natural sciences, Biochemistry, High-Resolution Relaxometry, 030218 nuclear medicine & medical imaging, 03 medical and health sciences, 0302 clinical medicine, Physics - Chemical Physics, Nuclear Spin Relaxation, [CHIM]Chemical Sciences, Statistical physics, Spin (physics), Chemical Physics (physics.chem-ph), Physics, Analytical expressions, Analytical Relaxation Computation, Condensed Matter Physics, Polarization (waves), 3. Good health, 0104 chemical sciences, Magnetic field
Abstract: A wide variety of nuclear magnetic resonance experiments rely on the prediction and analysis of relaxation processes. Recently, innovative approaches have been introduced where the sample travels through a broad range of magnetic fields in the course of the experiment, such as dissolution dynamic nuclear polarization or high-resolution relaxometry. Understanding the relaxation properties of nuclear spin systems over orders of magnitude of magnetic fields is essential to rationalize the results of these experiments. For example, during a high-resolution relaxometry experiment, the absence of control of nuclear spin relaxation pathways during the sample transfers and relaxation delays leads to systematic deviations of polarization decays from an ideal mono-exponential decay with the pure longitudinal relaxation rate. These deviations have to be taken into account to describe quantitatively the dynamics of the system. Here, we present computational tools to (1) calculate analytical expressions of relaxation rates for a broad variety of spin systems and (2) use these analytical expressions to correct the deviations arising in high-resolution relaxometry experiments. These tools lead to a better understanding of nuclear spin relaxation, which is required to improve the sensitivity of many pulse sequences, and to better characterize motions in macromolecules., 39 pages (and 22 pages of Supplementary Materials), 10 figures
Published: 2020

36. Determination of Protein ps-ns Motions by High-Resolution Relaxometry

Author: Samuel F. Cousin, Fabien Ferrage, Pavel Kadeřávek, Nicolas Bolik-Coulon, Structure et Dynamique des Biomolécules (LBM-E3), Laboratoire des biomolécules (LBM UMR 7203), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC), Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), and Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: Relaxometry, Materials science, Spectrometer, 010405 organic chemistry, Protein dynamics, Relaxation (NMR), Rotational diffusion, Nanosecond, 010402 general chemistry, 01 natural sciences, Molecular physics, 0104 chemical sciences, Magnetic field, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Nuclear magnetic resonance, Picosecond, ComputingMilieux_MISCELLANEOUS
Abstract: Many of the functions of biomacromolecules can be rationalized by the characterization of their conformational energy landscapes: the structures of the dominant states, transitions between states and motions within states. Nuclear magnetic resonance (NMR) spectroscopy is the technique of choice to study internal motions in proteins. The determination of motions on picosecond to nanosecond timescales requires the measurement of nuclear spin relaxation rates at multiple magnetic fields. High sensitivity and resolution are obtained only at high magnetic fields, so that, until recently, site-specific relaxation rates in biomolecules were only measured over a narrow range of high magnetic fields. This limitation was particularly striking for the quantification of motions on nanosecond timescales, close to the correlation time for overall rotational diffusion. High-resolution relaxometry is an emerging technique to investigate picosecond-nanosecond motions of proteins. This approach uses a high-field NMR spectrometer equipped with a sample shuttle device, which allows for the measurement of the relaxation rate constants at low magnetic fields, while preserving the sensitivity and resolution of a high-field NMR spectrometer. The combined analysis of high-resolution relaxometry and standard high-field relaxation data provides a more accurate description of the dynamics of proteins, in particular in the nanosecond range. The purpose of this chapter is to describe how to perform high-resolution relaxometry experiments and how to analyze the rates measured with this technique.
Published: 2018

37. Measuring Solvent Hydrogen Exchange Rates by Multifrequency Excitation 15 N CEST: Application to Protein Phase Separation

Author: Tairan Yuwen, Alaji Bah, Guillaume Bouvignies, Lewis E. Kay, Jacob P. Brady, Fabien Ferrage, Department of Chemistry, Purdue University [West Lafayette], Structure et Dynamique des Biomolécules (LBM-E3), Laboratoire des biomolécules (LBM UMR 7203), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: 0301 basic medicine, chemistry.chemical_classification, Hydrogen exchange, Materials science, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Biomolecule, [SDV]Life Sciences [q-bio], Protein domain, 010402 general chemistry, 01 natural sciences, 0104 chemical sciences, Surfaces, Coatings and Films, Solvent, 03 medical and health sciences, Magnetization, 030104 developmental biology, chemistry, Deuterium, Chemical physics, Phase (matter), Materials Chemistry, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Physical and Theoretical Chemistry, Excitation, ComputingMilieux_MISCELLANEOUS
Abstract: Solvent exchange rates provide important information about the structural and dynamical properties of biomolecules. A large number of NMR experiments have been developed to measure such rates in proteins, the great majority of which quantify the buildup of signals from backbone amides after initial perturbation of water magnetization. Here we present a different approach that circumvents the main limitations that result from these classical hydrogen exchange NMR experiments. Building on recent developments that enable rapid recording of chemical exchange saturation transfer (CEST) pseudo-3D data sets, we describe a 15N-based CEST scheme for measurement of solvent exchange in proteins that exploits the one-bond 15N deuterium isotope shift. The utility of the approach is verified with an application to a 236 residue intrinsically disordered protein domain under conditions where it phase separates and a second application involving a mutated form of the domain that does not phase separate, establishing very ...
Published: 2018

38. Field-cycling long-lived-state NMR of 15N2 spin pairs

Author: Malcolm H. Levitt, Daniel J. O'Leary, Pavel Kadeřávek, Stuart J. Elliott, Fabien Ferrage, Stefan Glöggler, Mohamed Sabba, Richard C. D. Brown, Lynda J. Brown, School of Chemistry [Southampton, UK], University of Southampton, Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Institut des Sciences Moléculaires (ISM), Université Montesquieu - Bordeaux 4-Université Sciences et Technologies - Bordeaux 1-École Nationale Supérieure de Chimie et de Physique de Bordeaux (ENSCPB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: Range (particle radiation), Materials science, 010304 chemical physics, Field cycling, Biophysics, Nuclear magnetic resonance spectroscopy, 010402 general chemistry, Condensed Matter Physics, 01 natural sciences, 0104 chemical sciences, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Magnetization, 0103 physical sciences, Physical and Theoretical Chemistry, Atomic physics, Spin (physics), Molecular Biology, ComputingMilieux_MISCELLANEOUS
Abstract: A range of nuclear magnetic resonance spectroscopy and imaging applications are limited by the short lifetimes of magnetisation in solution. Long-lived states, which are slowly relaxing configurations of nuclear spins, have been shown to alleviate this limitation. Long-lived states have decay lifetimes TLLS significantly exceeding the longitudinal relaxation time T1, in some cases by an order of magnitude. Here we present an experimental case of a long-lived state for a 15N labelled molecular system in solution. We observe a strongly biexponential decay for the long-lived state, with the lifetime of the slowly relaxing component exceeding 40 minutes, ∼21 times longer than the spin-lattice relaxation time T1. The lifetime of the long-lived state was revealed by using a dedicated two-field NMR spectrometer capable of fast sample shuttling between high and low magnetic fields, and the application of a resonant radiofrequency field at low magnetic field. The relaxation characteristics of the long-lived state are examined.
Published: 2018

39. High-Resolution NMR of Folded Proteins in Hyperpolarized Physiological Solvents

Author: Dennis Kurzbach, Geoffrey Bodenhausen, Pavel Kadeřávek, Fabien Ferrage, Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Masaryk University [Brno] (MUNI), Structure et Dynamique des Biomolécules (LBM-E3), Laboratoire des biomolécules (LBM UMR 7203), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Chimie Moléculaire de Paris Centre (FR 2769), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: 0301 basic medicine, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Chemistry, Organic Chemistry, General Chemistry, 010402 general chemistry, Photochemistry, 01 natural sciences, Catalysis, Spectral line, 0104 chemical sciences, Solvent, 03 medical and health sciences, chemistry.chemical_compound, 030104 developmental biology, Amide, Molecule, Target protein, Hyperpolarization (physics), Two-dimensional nuclear magnetic resonance spectroscopy, Dissolution
Abstract: International audience; Hyperpolarized 2D exchange spectroscopy (HYPEX) to obtain high‐resolution nuclear magnetic resonance (NMR) spectra of folded proteins under near‐physiological conditions is reported. The technique is based on hyperpolarized water, which is prepared by dissolution dynamic nuclear polarization and mixed in situ in an NMR spectrometer with a protein in a physiological saline buffer at body temperature. Rapid exchange of labile protons with the hyperpolarized solvent, combined with cross‐relaxation effects (NOEs), leads to boosted signal intensities for many amide 1H–15N correlations in the protein ubiquitin. As the introduction of hyperpolarization to the target protein is mediated via the solvent, the method is applicable to a broad spectrum of target molecules.
Published: 2018

40. Determination of Protein ps-ns Motions by High-Resolution Relaxometry

Author: Samuel F, Cousin, Pavel, Kadeřávek, Nicolas, Bolik-Coulon, and Fabien, Ferrage
Subjects: Models, Molecular, Motion, Magnetic Resonance Spectroscopy, Protein Conformation, Proteins
Abstract: Many of the functions of biomacromolecules can be rationalized by the characterization of their conformational energy landscapes: the structures of the dominant states, transitions between states and motions within states. Nuclear magnetic resonance (NMR) spectroscopy is the technique of choice to study internal motions in proteins. The determination of motions on picosecond to nanosecond timescales requires the measurement of nuclear spin relaxation rates at multiple magnetic fields. High sensitivity and resolution are obtained only at high magnetic fields, so that, until recently, site-specific relaxation rates in biomolecules were only measured over a narrow range of high magnetic fields. This limitation was particularly striking for the quantification of motions on nanosecond timescales, close to the correlation time for overall rotational diffusion. High-resolution relaxometry is an emerging technique to investigate picosecond-nanosecond motions of proteins. This approach uses a high-field NMR spectrometer equipped with a sample shuttle device, which allows for the measurement of the relaxation rate constants at low magnetic fields, while preserving the sensitivity and resolution of a high-field NMR spectrometer. The combined analysis of high-resolution relaxometry and standard high-field relaxation data provides a more accurate description of the dynamics of proteins, in particular in the nanosecond range. The purpose of this chapter is to describe how to perform high-resolution relaxometry experiments and how to analyze the rates measured with this technique.
Published: 2017

41. Chapter 4. Cross-correlation in Biomolecules

Author: Kavita Dorai, Fabien Ferrage, and Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: chemistry.chemical_classification, Physics, Quantitative Biology::Biomolecules, 0303 health sciences, Cross-correlation, Biomolecule, 010402 general chemistry, 01 natural sciences, 0104 chemical sciences, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, 03 medical and health sciences, Formalism (philosophy of mathematics), chemistry, Statistical physics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract: This chapter focuses on the methods used to quantitatively measure auto- and cross-correlated cross-relaxation relaxation rates in biomolecules and interpret these rates in terms of structure and dynamics. A theoretical description of average Liouvillian theory is presented in the beginning, to set the stage for understanding various experiments used to measure cross-relaxation in biomolecules. A series of multidimensional experiments to measure CSA–dipole, dipole–dipole, and CSA–CSA cross-correlations in large biomolecules such as proteins are discussed. Cross-correlated nuclear spin relaxation rates provide rich information about slow correlated motions as well as fast and slow internal motions in proteins. The next part of this chapter deals with motional models used to quantify cross-correlations. The model-free formalism and correlated internal motions are described in detail. A highlight of this chapter is an overview of the different cross-correlation parameters that can be obtained from dynamics studies. Several examples of applications of measurements of cross-correlation rates are then described, with special attention to proteins, nucleic acids and ligand-binding studies. The chapter concludes with a description of the famous TROSY experiments in biomolecules, which are based on CSA–dipole and dipole–dipole cross-correlations.
Published: 2017

42. High-Resolution Two-Field Nuclear Magnetic Resonance Spectroscopy

Author: Thorsten Marquardsen, Simone Ulzega, Cyril Charlier, Frank Engelke, Pierre-Alain Bovier, Werner Maas, Pavel Kadeřávek, Dimitrios Sakellariou, Thomas Speck, Philippe Pelupessy, Geoffrey Bodenhausen, Fabien Ferrage, Dirk Wilhelm, Samuel F. Cousin, Jean-Max Tyburn, Structure et Dynamique des Biomolécules (LBM-E3), Laboratoire des biomolécules (LBM UMR 7203), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC), Bruker BioSpin GmbH, D-76287 Rheinstetten, Germany, affiliation inconnue, Bruker BioSpin [Wissembourg], Bruker Biospin AG, Bruker BioSpin [Billerica, MA], Laboratoire Structure et Dynamique par Résonance Magnétique (LCF) (LSDRM), Nanosciences et Innovation pour les Matériaux, la Biomédecine et l'Energie (ex SIS2M) (NIMBE UMR 3685), Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), ANR-11-BS07-0031,DYN-IDP,Protéines : cinétique et désordre.(2011), European Project: 279519,EC:FP7:ERC,ERC-2011-StG_20101014,2F4BIODYN(2012), Université Pierre et Marie Curie - Paris 6 (UPMC)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Département de Chimie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Condensed matter physics, Chemistry, 530: Physik, General Physics and Astronomy, Magnetic resonance force microscopy, 02 engineering and technology, Nuclear magnetic resonance spectroscopy, [CHIM.MATE]Chemical Sciences/Material chemistry, 010402 general chemistry, 021001 nanoscience & nanotechnology, Magnetostatics, 01 natural sciences, Molecular physics, 0104 chemical sciences, Solid-state nuclear magnetic resonance, Spin echo, Transverse relaxation-optimized spectroscopy, Physical and Theoretical Chemistry, 0210 nano-technology, Two-dimensional nuclear magnetic resonance spectroscopy, Earth's field NMR
Abstract: Nuclear magnetic resonance (NMR) is a ubiquitous branch of spectroscopy that can explore matter at the scale of an atom. Significant improvements in sensitivity and resolution have been driven by a steady increase of static magnetic field strengths. However, some properties of nuclei may be more favourable at low magnetic fields. For example, transverse relaxation due to chemical shift anisotropy increases sharply at higher magnetic fields leading to line-broadening and inefficient coherence transfers. Here, we present a two-field NMR spectrometer that permits the application of rf-pulses and acquisition of NMR signals in two magnetic centres. Our prototype operates at 14.1 T and 0.33 T. The main features of this system are demonstrated by novel NMR experiments, in particular a proof-of-concept correlation between zero-quantum coherences at low magnetic field and single quantum coherences at high magnetic field, so that high resolution can be achieved in both dimensions, despite a ca. 10 ppm inhomogeneity of the low-field centre. Two-field NMR spectroscopy offers the possibility to circumvent the limits of high magnetic fields, while benefiting from their exceptional sensitivity and resolution. This approach opens new avenues for NMR above 1 GHz.
Published: 2016
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43. Sample Shuttling Relaxometry of Contrast Agents: NMRD Profiles above 1 T with a Single Device

Author: Thorsten Marquardsen, Yves Gossuin, Zeinab Serhan, Rafael Torres Martin de Rosales, Lydia Sandiford, Fabien Ferrage, Daniel Henrard, Dimitrios Sakellariou, Biomedical Physics Department, Université Pierre et Marie Curie - Paris 6 (UPMC), Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Imaging Sciences and Biomedical Engineering Division [London], Guy's and St Thomas' Hospital [London]-King‘s College London, Bruker Biospin GmbH, bruker, Laboratoire Structure et Dynamique par Résonance Magnétique (LCF) (LSDRM), Nanosciences et Innovation pour les Matériaux, la Biomédecine et l'Energie (ex SIS2M) (NIMBE UMR 3685), Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), European Project: 279519,EC:FP7:ERC,ERC-2011-StG_20101014,2F4BIODYN(2012), École normale supérieure - Paris (ENS-PSL), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Rayonnement Matière de Saclay (IRAMIS), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Larmor precession, Relaxometry, Gadolinium, Relaxation (NMR), Spin–lattice relaxation, chemistry.chemical_element, 02 engineering and technology, 010402 general chemistry, 021001 nanoscience & nanotechnology, equipment and supplies, 01 natural sciences, Article, Atomic and Molecular Physics, and Optics, 0104 chemical sciences, Paramagnetism, Nuclear magnetic resonance, chemistry, Magnet, Magnetic nanoparticles, [SDV.IB]Life Sciences [q-bio]/Bioengineering, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], 0210 nano-technology, human activities
Abstract: Nuclear magnetic relaxation dispersion (NMRD) profiles are essential tools to evaluate the efficiency and investigate the properties of magnetic compounds used as contrast agents for magnetic resonance imaging (MRI), namely gadolinium chelates and superparamagnetic iron oxide particles. These curves represent the evolution of proton relaxation rates with the magnetic field. NMRD profiles are unparalleled to probe extensively the spectral density function involved in the relaxation of water in the presence of the paramagnetic ion or the magnetic nanoparticles. This makes such profiles an excellent test of the adequacy of a theoretical relaxation model and allow for a predictive approach to the development and optimization of contrast agents. From a practical point of view they also allow to evaluate the efficiency of a contrast agent in a certain range of magnetic fields. Nowadays, these curves are recorded with commercial fast field cycling devices, often limited to a maximum Larmor frequency of 40 MHz (0.94 T). In this article, relaxation data were acquired on a wide range of magnetic fields, from 3.5 × 10−4 to 14 T, for a gadolinium-based contrast agent and for PEGylated iron oxide nanoparticles. We show that the low-field NMRD curves can be completed with high-field data obtained on a shuttle apparatus device using the superconductive magnet of a high-field spectrometer. This allows a better characterization of the contrast agents at relevant magnetic fields for clinical and preclinical MRI, but also refines the experimental data that could be used for the validation of relaxation models. Electronic supplementary material The online version of this article (doi:10.1007/s00723-015-0751-7) contains supplementary material, which is available to authorized users.
Published: 2016

44. Identification of Hydrophobic Interfaces in Protein-Ligand Complexes by Selective Saturation Transfer NMR Spectroscopy

Author: David Cowburn, Kaushik Dutta, Fabien Ferrage, Université Pierre et Marie Curie - Paris 6 (UPMC), Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), New York Structural Biology Center (NYSBC), Columbia University [New York]-Wadsworth Center, New York State Department of Health [Albany]-New York State Department of Health [Albany]-New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU)-City University of New York [New York] (CUNY)-Rockefeller University [New York]-Memorial Sloane Kettering Cancer Center [New York]-Icahn School of Medicine at Mount Sinai [New York] (MSSM)- Albert Einstein College of Medicine [New York]-Weill Medical College of Cornell University [New York], Albert Einstein College of Medicine [New York], and École normale supérieure - Paris (ENS Paris)
Subjects: Models, Molecular, Pharmaceutical Science, Peptide, SH3 ligand, Protein tyrosine phosphatase, 010402 general chemistry, Bioinformatics, Ligands, 01 natural sciences, SH3 domain, Article, Analytical Chemistry, lcsh:QD241-441, Isotopic labeling, CSK Tyrosine-Protein Kinase, src Homology Domains, 03 medical and health sciences, lcsh:Organic chemistry, Drug Discovery, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, Physical and Theoretical Chemistry, Nuclear Magnetic Resonance, Biomolecular, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Binding Sites, Organic Chemistry, Nuclear magnetic resonance spectroscopy, Peptide Fragments, NMR, 0104 chemical sciences, src-Family Kinases, interface identification, Structural biology, chemistry, Chemistry (miscellaneous), cross-saturation, Biophysics, Molecular Medicine, Protein Tyrosine Phosphatases, Hydrophobic and Hydrophilic Interactions, Protein ligand, Proto-oncogene tyrosine-protein kinase Src, Protein Binding
Abstract: International audience; The proper characterization of protein-ligand interfaces is essential for structural biology, with implications ranging from the fundamental understanding of biological processes to pharmacology. Nuclear magnetic resonance is a powerful technique for such studies. We propose a novel approach to the direct determination of the likely pose of a peptide ligand onto a protein partner, by using frequency-selective cross-saturation with a low stringency isotopic labeling methods. Our method illustrates a complex of the Src homology 3 domain of C-terminal Src kinase with a peptide from the proline-enriched tyrosine phosphatase.
Published: 2015
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45. On the measurement of 15N–{1H} nuclear Overhauser effects. 2. Effects of the saturation scheme and water signal suppression

Author: Shibani Battacharya, Ranajeet Ghose, Amy Reichel, Fabien Ferrage, and David Cowburn
Subjects: 0303 health sciences, Nuclear and High Energy Physics, Chemistry, Protein dynamics, Biophysics, Nuclear magnetic resonance spectroscopy, Nuclear Overhauser effect, Radiation, 010402 general chemistry, Condensed Matter Physics, Residual, 01 natural sciences, Biochemistry, Signal, 0104 chemical sciences, 03 medical and health sciences, Nuclear magnetic resonance, Radiation damping, Atomic physics, Saturation (chemistry), 030304 developmental biology
Abstract: Measurement of steady-state (15)N-{(1)H} nuclear Overhauser effects forms a cornerstone of most methods to determine protein backbone dynamics from spin-relaxation data, since it is the most reliable probe of very fast motions on the ps-ns timescale. We have, in two previous publications (J. Magn. Reson. 192 (2008) 302-313; J. Am. Chem. Soc. 131 (2009) 6048-6049) reevaluated spin-dynamics during steady-state (or "saturated") and reference experiments, both of which are required to determine the NOE ratio. Here we assess the performance of several windowed and windowless sequences to achieve effective saturation of protons in steady-state experiments. We also evaluate the influence of the residual water signal due to radiation damping on the NOE ratio. We suggest a recipe that allows one to determine steady-state (15)N-{(1)H} NOE's without artifacts and with the highest possible accuracy.
Published: 2010

46. Structural determination of biomolecular interfaces by nuclear magnetic resonance of proteins with reduced proton density

Author: Alexander Shekhtman, Kaushik Dutta, David Cowburn, Fabien Ferrage, Biomolécules : synthèse, structure et mode d'action (UMR 8642) (BIOSYMA), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC), New York Structural Biology Center (NYSBC), Columbia University [New York]-Wadsworth Center, New York State Department of Health [Albany]-New York State Department of Health [Albany]-New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU)-City University of New York [New York] (CUNY)-Rockefeller University [New York]-Memorial Sloane Kettering Cancer Center [New York]-Icahn School of Medicine at Mount Sinai [New York] (MSSM)- Albert Einstein College of Medicine [New York]-Weill Medical College of Cornell University [New York], Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: Models, Molecular, 010402 general chemistry, 01 natural sciences, Biochemistry, Article, Partial deuteration, Protein–protein interaction, 03 medical and health sciences, Nuclear magnetic resonance, Csk SH3, Protein Interaction Mapping, Computer Simulation, Spectroscopy, Nuclear Magnetic Resonance, Biomolecular, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Binding Sites, Ubiquitin, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Biomolecule, Intermolecular force, Proteins, Protein complex, Nuclear magnetic resonance spectroscopy, 0104 chemical sciences, Isotope-filtered NOESY, chemistry, Docking (molecular), Cross-relaxation, Target protein, Protons, Monte Carlo Method, Two-dimensional nuclear magnetic resonance spectroscopy
Abstract: International audience; Protein interactions are important for understanding many molecular mechanisms underlying cellular processes. So far, interfaces between interacting proteins have been characterized by NMR spectroscopy mostly by using chemical shift perturbations and cross-saturation via intermolecular cross-relaxation. Although powerful, these techniques cannot provide unambiguous estimates of intermolecular distances between interacting proteins. Here, we present an alternative approach, called REDSPRINT (REDduced/Standard PRoton density INTerface identification), to map protein interfaces with greater accuracy by using multiple NMR probes. Our approach is based on monitoring the cross-relaxation from a source protein (or from an arbitrary ligand that need not be a protein) with high proton density to a target protein (or other biomolecule) with low proton density by using isotope-filtered nuclear Overhauser spectroscopy (NOESY). This methodology uses different isotropic labeling for the source and target proteins to identify the source-target interface and also determine the proton density of the source protein at the interface for protein-protein or protein-ligand docking. Simulation indicates significant gains in sensitivity because of the resultant relaxation properties, and the utility of this technique, including a method for direct determination of the protein interface, is demonstrated for two different protein-protein complexes.
Published: 2010

47. Single or triple gradients?

Author: Detlef Moskau, Geoffrey Bodenhausen, Riddhiman Sarkar, Fabien Ferrage, and Paul R. Vasos
Subjects: Nuclear and High Energy Physics, Nuclear magnetic resonance, Chemistry, Chemical physics, Slow exchange, Biophysics, Spatial encoding, Singlet state, Condensed Matter Physics, Spectroscopy, Biochemistry, Two-dimensional nuclear magnetic resonance spectroscopy, Coherence (physics)
Abstract: Pulsed Field Gradients (PFGs) have become ubiquitous tools not only for Magnetic Resonance Imaging (MRI), but also for NMR experiments designed to study translational diffusion, for spatial encoding in ultra-fast spectroscopy, for the selection of desirable coherence transfer pathways, for the suppression of solvent signals, and for the elimination of zero-quantum coherences. Some of these experiments can only be carried out if three orthogonal gradients are available, while others can also be implemented using a single gradient, albeit at some expense of performance. This paper discusses some of the advantages of triple- with respect to single-gradient probes. By way of examples we discuss (i) the measurement of small diffusion coefficients making use of the long spin-lattice relaxation times of nuclei with low gyromagnetic ratios gamma such as nitrogen-15, and (ii) the elimination of zero-quantum coherences in Exchange or Nuclear Overhauser Spectroscopy (EXSY or NOESY) experiments, as well as in methods relying on long-lived (singlet) states to study very slow exchange or diffusion processes.
Published: 2008

48. Nuclear overhauser spectroscopy of chiral CHD methylene groups

Author: Geoffrey Bodenhausen, Henri Colaux, Jan Stanek, Torsten Herrmann, Fabien Ferrage, Rafal Augustyniak, Wiktor Koźmiński, Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Université Pierre et Marie Curie - Paris 6 (UPMC), Biological Solid-State NMR Methods - Méthodes de RMN à l'état solide en biologie, Institut des Sciences Analytiques (ISA), Institut de Chimie du CNRS (INC)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Computational Methods for Biomolecular Studies, European Commission [228461], Bio-NMR Project [261863], [IP2012 057872], École normale supérieure - Paris (ENS-PSL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Models, Molecular, Molecular Conformation, Nuclear Overhauser effect, 010402 general chemistry, 01 natural sciences, Biochemistry, Nuclear Overhauser spectroscopy, 03 medical and health sciences, chemistry.chemical_compound, Nuclear magnetic resonance, Protein structure, NMR spectroscopy, S100 Calcium Binding Protein G, Computational chemistry, Protein structures, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Methylene, Spectroscopy, Nuclear Magnetic Resonance, Biomolecular, chemistry.chemical_classification, Chemistry, Biomolecule, Proteins, Nuclear magnetic resonance spectroscopy, 0104 chemical sciences, Automatic structure calculation, 030104 developmental biology, Deuterium, Two-dimensional nuclear magnetic resonance spectroscopy
Abstract: International audience; Nuclear magnetic resonance spectroscopy (NMR) can provide a great deal of information about structure and dynamics of biomolecules. The quality of an NMR structure strongly depends on the number of experimental observables and on their accurate conversion into geometric restraints. When distance restraints are derived from nuclear Overhauser effect spectroscopy (NOESY), stereo-specific assignments of prochiral atoms can contribute significantly to the accuracy of NMR structures of proteins and nucleic acids. Here we introduce a series of NOESY-based pulse sequences that can assist in the assignment of chiral CHD methylene protons in random fractionally deuterated proteins. Partial deuteration suppresses spin-diffusion between the two protons of CH2 groups that normally impedes the distinction of cross-relaxation networks for these two protons in NOESY spectra. Three and four-dimensional spectra allow one to distinguish cross-relaxation pathways involving either of the two methylene protons so that one can obtain stereospecific assignments. In addition, the analysis provides a large number of stereospecific distance restraints. Non-uniform sampling was used to ensure optimal signal resolution in 4D spectra and reduce ambiguities of the assignments. Automatic assignment procedures were modified for efficient and accurate stereospecific assignments during automated structure calculations based on 3D spectra. The protocol was applied to calcium-loaded calbindin D-9k. A large number of stereospecific assignments lead to a significant improvement of the accuracy of the structure.
Published: 2015

49. Cross-correlated relaxation measurements under adiabatic sweeps: determination of local order in proteins

Author: Pavel Kadeřávek, Sarina Grutsch, Nicola Salvi, Martin Tollinger, Lukáš Žídek, Geoffrey Bodenhausen, Fabien Ferrage
Published: 2015
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50. Simple method for the generation of multiple homogeneous field volumes inside the bore of superconducting magnets

Author: Dimitrios Sakellariou, Ching-Yu Chou, Fabien Ferrage, Guy Aubert, Laboratoire Structure et Dynamique par Résonance Magnétique (LCF) (LSDRM), Nanosciences et Innovation pour les Matériaux, la Biomédecine et l'Energie (ex SIS2M) (NIMBE UMR 3685), Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut Rayonnement Matière de Saclay (IRAMIS), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)
Subjects: Multidisciplinary, Field (physics), Series (mathematics), 010405 organic chemistry, Computer science, Demagnetizing field, Superconducting magnet, 010402 general chemistry, computer.software_genre, 01 natural sciences, Article, 0104 chemical sciences, Magnetic field, Computational physics, Applied physics, [SPI.ELEC]Engineering Sciences [physics]/Electromagnetism, Chemical engineering, NMR spectroscopy, Magnet, Data mining, computer, Volume (compression)
Abstract: Standard Magnetic Resonance magnets produce a single homogeneous field volume, where the analysis is performed. Nonetheless, several modern applications could benefit from the generation of multiple homogeneous field volumes along the axis and inside the bore of the magnet. In this communication, we propose a straightforward method using a combination of ring structures of permanent magnets in order to cancel the gradient of the stray field in a series of distinct volumes. These concepts were demonstrated numerically on an experimentally measured magnetic field profile. We discuss advantages and limitations of our method and present the key steps required for an experimental validation.
Published: 2015

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